src/mdParser/MDTreeParser.g

header
{
#include <stack>
#include "io/Globals.hpp"
#include "utils/StringUtils.hpp"
using namespace std;
using namespace OpenMD;
}
options
  {
  language = "Cpp";
  }
                     
class MDTreeParser extends TreeParser;

options
{
        k = 1;
        importVocab = MD;
}
{
  public:
    Globals* walkTree(ANTLR_USE_NAMESPACE(antlr)RefAST tree)
    {
      currConf = new Globals;
      blockStack.push(currConf);
      mdfile(tree);
      return currConf;
    }
  private:
    Globals* currConf;
    stack<DataHolder*> blockStack;    
}
mdfile  : (statement)* {blockStack.top()->validate(); blockStack.pop();}
        ;

statement : assignment
    | componentblock
    | moleculeblock
    | zconstraintblock
    | restraintblock
    | flucqblock
    | rnemdblock
    | minimizerblock
    ;

assignment  : #(ASSIGNEQUAL id:ID constant[#id]) //{blockStack.top()->assign(#ID->getText(),);}
            ;
            
constant [ANTLR_USE_NAMESPACE(antlr)RefAST id]
{
    int ival;
    RealType dval, x, y, z;
    Vector3d dvec;
}    
    : ival=intConst {blockStack.top()->assign(id->getText(), ival);}
    | dval=floatConst {blockStack.top()->assign(id->getText(), dval);}
    | #(LPAREN x=doubleNumber COMMA y=doubleNumber COMMA z=doubleNumber RPAREN) 
        {   dvec.x() = x; 
            dvec.y() = y; 
            dvec.z() = z; 
            blockStack.top()->assign(id->getText(), dvec);
        }
    | str1:ID {blockStack.top()->assign(id->getText(), str1->getText());}
    | str2:StringLiteral {std::string s =  str2->getText();
            s = s.substr(1, s.length()-2);
            blockStack.top()->assign(id->getText(),s);
        }
    ;
            

componentblock  : #(COMPONENT  {Component* currComponet = new Component(); blockStack.push(currComponet);}
                      (assignment)* 
                       ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addComponent(currComponet);}
                ;
    
zconstraintblock  : #(ZCONSTRAINT {ZConsStamp* currZConsStamp = new ZConsStamp(); blockStack.push(currZConsStamp);}
                        (assignment)* 
                         ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addZConsStamp(currZConsStamp);}
                  ;

restraintblock  : #(RESTRAINT {RestraintStamp* currRestraintStamp = new RestraintStamp(); blockStack.push(currRestraintStamp);}
                        (assignment)* 
                         ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addRestraintStamp(currRestraintStamp);}
                  ;
  
flucqblock  : #(FLUCQ  {FluctuatingChargeParameters* flucQpars = new FluctuatingChargeParameters(); blockStack.push(flucQpars);}
                      (assignment)* 
                       ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addFluctuatingChargeParameters(flucQpars);}
                ;

rnemdblock  : #(RNEMD  {RNEMDParameters* rnemdPars = new RNEMDParameters(); blockStack.push(rnemdPars);}
                      (assignment)* 
                       ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addRNEMDParameters(rnemdPars);}
                ;

minimizerblock  : #(MINIMIZER  {MinimizerParameters* minimizerPars = new MinimizerParameters(); blockStack.push(minimizerPars);}
                      (assignment)* 
                       ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addMinimizerParameters(minimizerPars);}
                ;


moleculeblock : #(MOLECULE {MoleculeStamp* currMoleculeStamp = new MoleculeStamp(); blockStack.push(currMoleculeStamp);}
                    (moleculestatement)* 
                     ENDBLOCK ) {blockStack.top()->validate(); blockStack.pop(); currConf->addMoleculeStamp(currMoleculeStamp);}
              ;

moleculestatement : assignment
                  | atomblock
                  | bondblock
                  | bendblock
                  | torsionblock
                  | inversionblock
                  | rigidbodyblock
                  | cutoffgroupblock
                  | fragmentblock
                  ;

atomblock 
{
  int index;
}
          : #(ATOM index=intConst {AtomStamp* currAtomStamp = new AtomStamp(index); blockStack.push(currAtomStamp);} 
                  (atomstatement)* 
                  ENDBLOCK ) {
                                blockStack.top()->validate();
                                blockStack.pop(); 
                                MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                currMoleculeStamp->addAtomStamp(currAtomStamp); 
                             }
          ;

atomstatement 
{
vector<RealType> dvec;
AtomStamp* currAtomStamp =  static_cast<AtomStamp*>(blockStack.top());

}
              : assignment
              | #(POSITION dvec=doubleNumberTuple) {currAtomStamp->setPosition(dvec);}
              | #(ORIENTATION dvec=doubleNumberTuple) {currAtomStamp->setOrientation(dvec);}
              ;

                      
bondblock : #(BOND {BondStamp* currBondStamp = new BondStamp(); blockStack.push(currBondStamp);}
                (bondstatement)* 
                 ENDBLOCK )  {
                                blockStack.pop(); 
                                MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                currMoleculeStamp->addBondStamp(currBondStamp); 
                             }
          ;

bondstatement 
{
  vector<int> ivec;
  BondStamp* currBondStamp = static_cast<BondStamp*>(blockStack.top());
}
              : assignment
              | #(MEMBERS ivec=inttuple) {currBondStamp->setMembers(ivec);}
              ;

bendblock : #(BEND {BendStamp* currBendStamp = new BendStamp(); blockStack.push(currBendStamp);}
                  (bendstatement)* 
                   ENDBLOCK)  {
                                blockStack.top()->validate();
                                blockStack.pop(); 
                                MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                currMoleculeStamp->addBendStamp(currBendStamp); 
                             }
          ;

bendstatement 
{
  vector<int> ivec;
  BendStamp* currBendStamp = static_cast<BendStamp*>(blockStack.top());
}
              : assignment
              | #(MEMBERS ivec=inttuple) {currBendStamp->setMembers(ivec);}
              ;

torsionblock  : #(TORSION {TorsionStamp* currTorsionStamp = new TorsionStamp(); blockStack.push(currTorsionStamp);}
                   (torsionstatement)*
                    ENDBLOCK )  {
                                  blockStack.top()->validate();
                                  blockStack.pop(); 
                                  MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                  currMoleculeStamp->addTorsionStamp(currTorsionStamp); 
                                }
          ;

torsionstatement
{
  vector<int> ivec;
  TorsionStamp* currTorsionStamp = static_cast<TorsionStamp*>(blockStack.top());
}  
              : assignment
              | #(MEMBERS ivec=inttuple) {currTorsionStamp->setMembers(ivec);}
              ;

inversionblock  : #(INVERSION {InversionStamp* currInversionStamp = new InversionStamp(); blockStack.push(currInversionStamp);}
                   (inversionstatement)*
                    ENDBLOCK )  {
                                  blockStack.top()->validate();
                                  blockStack.pop(); 
                                  MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                  currMoleculeStamp->addInversionStamp(currInversionStamp); 
                                }
          ;

inversionstatement
{
  int icent;
  InversionStamp* currInversionStamp = static_cast<InversionStamp*>(blockStack.top());
}  
              : assignment
              | #(CENTER icent=intConst) {currInversionStamp->setCenter(icent);}
              ;

rigidbodyblock
{
int index;
}
              : #(RIGIDBODY index=intConst {RigidBodyStamp* currRigidBodyStamp = new RigidBodyStamp(index); blockStack.push(currRigidBodyStamp);}
                        (rigidbodystatement)* 
                        ENDBLOCK )  {
                                      blockStack.top()->validate();
                                      blockStack.pop(); 
                                      MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                      currMoleculeStamp->addRigidBodyStamp(currRigidBodyStamp); 
                                    }
                ;

rigidbodystatement  
{
  vector<int> ivec;
  RigidBodyStamp* currRigidBodyStamp = static_cast<RigidBodyStamp*>(blockStack.top());
}
              : assignment
              | #(MEMBERS ivec=inttuple) {currRigidBodyStamp->setMembers(ivec);}
              ;

cutoffgroupblock  : #(CUTOFFGROUP  {CutoffGroupStamp* currCutoffGroupStamp = new CutoffGroupStamp(); blockStack.push(currCutoffGroupStamp);}
                          (cutoffgroupstatement)* 
                           ENDBLOCK ) {
                                        blockStack.top()->validate();
                                        blockStack.pop(); 
                                        MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                        currMoleculeStamp->addCutoffGroupStamp(currCutoffGroupStamp); 
                                      }
                  ;

cutoffgroupstatement
{
  vector<int> ivec;
  CutoffGroupStamp* currCutoffGroupStamp = static_cast<CutoffGroupStamp*>(blockStack.top());
}  
              : assignment
              | #(MEMBERS ivec=inttuple) {currCutoffGroupStamp->setMembers(ivec);}             
              ;

fragmentblock {int ival;}
               : #(FRAGMENT ival=intConst {FragmentStamp* currFragmentStamp = new FragmentStamp(ival); blockStack.push(currFragmentStamp);}
                      (fragmentstatement)* 
                      ENDBLOCK) {
                                  blockStack.top()->validate();
                                  blockStack.pop(); 
                                  MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
                                  currMoleculeStamp->addFragmentStamp(currFragmentStamp); 
                                }
              ;

fragmentstatement : assignment
    ;


doubleNumberTuple returns [vector<RealType> dvec]
{
    RealType dval;
}   
    : (dval=doubleNumber {dvec.push_back(dval);})+  
    ;


inttuple returns [vector<int> ivec]
{
    int ival;
}
    : (ival=intConst {ivec.push_back(ival);})+ 
    ;

protected
intConst returns [int ival]
    : i1:NUM_INT {ival = lexi_cast<int>(i1->getText());} 
    | i2:NUM_LONG {ival = lexi_cast<int>(i2->getText());}
    ;

protected
doubleNumber returns [RealType dval]
    : ic:intConst {dval = lexi_cast<RealType>(ic->getText());}
    | fc:floatConst {dval = lexi_cast<RealType>(fc->getText());}         
    ;
              
protected
floatConst returns [RealType dval]
    : d1:NUM_FLOAT {dval = lexi_cast<RealType>(d1->getText());}  
    | d2:NUM_DOUBLE {dval = lexi_cast<RealType>(d2->getText());} 
    ;
  
Revision:	1776
Committed:	Thu Aug 9 15:52:59 2012 UTC (12 years, 8 months ago) by gezelter
File size:	11751 byte(s)
Log Message:	Fixes to mdParser to handle vector assignments, fixes for VelocityVerletIntegrator deleting rnemd_ when it doesn't exist yet.
#	User	Rev	Content
1	tim	770	header
2			{
3			#include <stack>
4			#include "io/Globals.hpp"
5			#include "utils/StringUtils.hpp"
6			using namespace std;
7	gezelter	1390	using namespace OpenMD;
8	tim	770	}
9			options
10			{
11			language = "Cpp";
12			}
13
14			class MDTreeParser extends TreeParser;
15
16			options
17			{
18	gezelter	1277	k = 1;
19	tim	770	importVocab = MD;
20			}
21			{
22			public:
23			Globals* walkTree(ANTLR_USE_NAMESPACE(antlr)RefAST tree)
24			{
25			currConf = new Globals;
26			blockStack.push(currConf);
27			mdfile(tree);
28			return currConf;
29			}
30			private:
31			Globals* currConf;
32			stack<DataHolder*> blockStack;
33			}
34			mdfile : (statement)* {blockStack.top()->validate(); blockStack.pop();}
35			;
36
37			statement : assignment
38	gezelter	1731	\| componentblock
39			\| moleculeblock
40			\| zconstraintblock
41			\| restraintblock
42			\| flucqblock
43			\| rnemdblock
44	gezelter	1746	\| minimizerblock
45	gezelter	1731	;
46	tim	770
47			assignment : #(ASSIGNEQUAL id:ID constant[#id]) //{blockStack.top()->assign(#ID->getText(),);}
48			;
49
50	tim	814	constant [ANTLR_USE_NAMESPACE(antlr)RefAST id]
51			{
52	gezelter	1776	int ival;
53			RealType dval, x, y, z;
54			Vector3d dvec;
55	tim	814	}
56	gezelter	1776	: ival=intConst {blockStack.top()->assign(id->getText(), ival);}
57			\| dval=floatConst {blockStack.top()->assign(id->getText(), dval);}
58			\| #(LPAREN x=doubleNumber COMMA y=doubleNumber COMMA z=doubleNumber RPAREN)
59			{ dvec.x() = x;
60			dvec.y() = y;
61			dvec.z() = z;
62			blockStack.top()->assign(id->getText(), dvec);
63			}
64			\| str1:ID {blockStack.top()->assign(id->getText(), str1->getText());}
65			\| str2:StringLiteral {std::string s = str2->getText();
66			s = s.substr(1, s.length()-2);
67			blockStack.top()->assign(id->getText(),s);
68			}
69			;
70	tim	770
71
72			componentblock : #(COMPONENT {Component* currComponet = new Component(); blockStack.push(currComponet);}
73			(assignment)*
74			ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addComponent(currComponet);}
75			;
76
77			zconstraintblock : #(ZCONSTRAINT {ZConsStamp* currZConsStamp = new ZConsStamp(); blockStack.push(currZConsStamp);}
78			(assignment)*
79			ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addZConsStamp(currZConsStamp);}
80			;
81	cli2	1360
82			restraintblock : #(RESTRAINT {RestraintStamp* currRestraintStamp = new RestraintStamp(); blockStack.push(currRestraintStamp);}
83			(assignment)*
84			ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addRestraintStamp(currRestraintStamp);}
85			;
86	tim	770
87	gezelter	1731	flucqblock : #(FLUCQ {FluctuatingChargeParameters* flucQpars = new FluctuatingChargeParameters(); blockStack.push(flucQpars);}
88			(assignment)*
89			ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addFluctuatingChargeParameters(flucQpars);}
90			;
91
92			rnemdblock : #(RNEMD {RNEMDParameters* rnemdPars = new RNEMDParameters(); blockStack.push(rnemdPars);}
93			(assignment)*
94			ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addRNEMDParameters(rnemdPars);}
95			;
96
97	gezelter	1746	minimizerblock : #(MINIMIZER {MinimizerParameters* minimizerPars = new MinimizerParameters(); blockStack.push(minimizerPars);}
98			(assignment)*
99			ENDBLOCK ) {blockStack.top()->validate();blockStack.pop(); currConf->addMinimizerParameters(minimizerPars);}
100			;
101	gezelter	1731
102	gezelter	1746
103	tim	770	moleculeblock : #(MOLECULE {MoleculeStamp* currMoleculeStamp = new MoleculeStamp(); blockStack.push(currMoleculeStamp);}
104			(moleculestatement)*
105			ENDBLOCK ) {blockStack.top()->validate(); blockStack.pop(); currConf->addMoleculeStamp(currMoleculeStamp);}
106			;
107
108			moleculestatement : assignment
109			\| atomblock
110			\| bondblock
111			\| bendblock
112			\| torsionblock
113	cli2	1275	\| inversionblock
114	tim	770	\| rigidbodyblock
115			\| cutoffgroupblock
116			\| fragmentblock
117			;
118
119			atomblock
120			{
121			int index;
122			}
123			: #(ATOM index=intConst {AtomStamp* currAtomStamp = new AtomStamp(index); blockStack.push(currAtomStamp);}
124			(atomstatement)*
125			ENDBLOCK ) {
126			blockStack.top()->validate();
127			blockStack.pop();
128			MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
129			currMoleculeStamp->addAtomStamp(currAtomStamp);
130			}
131			;
132
133			atomstatement
134			{
135	tim	963	vector<RealType> dvec;
136	tim	770	AtomStamp* currAtomStamp = static_cast<AtomStamp*>(blockStack.top());
137
138			}
139			: assignment
140	tim	814	\| #(POSITION dvec=doubleNumberTuple) {currAtomStamp->setPosition(dvec);}
141			\| #(ORIENTATION dvec=doubleNumberTuple) {currAtomStamp->setOrientation(dvec);}
142	tim	770	;
143
144
145			bondblock : #(BOND {BondStamp* currBondStamp = new BondStamp(); blockStack.push(currBondStamp);}
146			(bondstatement)*
147			ENDBLOCK ) {
148			blockStack.pop();
149			MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
150			currMoleculeStamp->addBondStamp(currBondStamp);
151			}
152			;
153
154			bondstatement
155			{
156			vector<int> ivec;
157			BondStamp* currBondStamp = static_cast<BondStamp*>(blockStack.top());
158			}
159			: assignment
160			\| #(MEMBERS ivec=inttuple) {currBondStamp->setMembers(ivec);}
161			;
162
163			bendblock : #(BEND {BendStamp* currBendStamp = new BendStamp(); blockStack.push(currBendStamp);}
164			(bendstatement)*
165			ENDBLOCK) {
166			blockStack.top()->validate();
167			blockStack.pop();
168			MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
169			currMoleculeStamp->addBendStamp(currBendStamp);
170			}
171			;
172
173			bendstatement
174			{
175			vector<int> ivec;
176			BendStamp* currBendStamp = static_cast<BendStamp*>(blockStack.top());
177			}
178			: assignment
179			\| #(MEMBERS ivec=inttuple) {currBendStamp->setMembers(ivec);}
180			;
181
182			torsionblock : #(TORSION {TorsionStamp* currTorsionStamp = new TorsionStamp(); blockStack.push(currTorsionStamp);}
183			(torsionstatement)*
184			ENDBLOCK ) {
185			blockStack.top()->validate();
186			blockStack.pop();
187			MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
188			currMoleculeStamp->addTorsionStamp(currTorsionStamp);
189			}
190			;
191
192			torsionstatement
193			{
194			vector<int> ivec;
195			TorsionStamp* currTorsionStamp = static_cast<TorsionStamp*>(blockStack.top());
196			}
197			: assignment
198			\| #(MEMBERS ivec=inttuple) {currTorsionStamp->setMembers(ivec);}
199			;
200
201	cli2	1275	inversionblock : #(INVERSION {InversionStamp* currInversionStamp = new InversionStamp(); blockStack.push(currInversionStamp);}
202			(inversionstatement)*
203			ENDBLOCK ) {
204			blockStack.top()->validate();
205			blockStack.pop();
206			MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
207			currMoleculeStamp->addInversionStamp(currInversionStamp);
208			}
209			;
210
211			inversionstatement
212			{
213			int icent;
214			InversionStamp* currInversionStamp = static_cast<InversionStamp*>(blockStack.top());
215			}
216			: assignment
217			\| #(CENTER icent=intConst) {currInversionStamp->setCenter(icent);}
218			;
219
220	tim	770	rigidbodyblock
221			{
222			int index;
223			}
224			: #(RIGIDBODY index=intConst {RigidBodyStamp* currRigidBodyStamp = new RigidBodyStamp(index); blockStack.push(currRigidBodyStamp);}
225			(rigidbodystatement)*
226			ENDBLOCK ) {
227			blockStack.top()->validate();
228			blockStack.pop();
229			MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
230			currMoleculeStamp->addRigidBodyStamp(currRigidBodyStamp);
231			}
232			;
233
234			rigidbodystatement
235			{
236			vector<int> ivec;
237			RigidBodyStamp* currRigidBodyStamp = static_cast<RigidBodyStamp*>(blockStack.top());
238			}
239			: assignment
240			\| #(MEMBERS ivec=inttuple) {currRigidBodyStamp->setMembers(ivec);}
241			;
242
243			cutoffgroupblock : #(CUTOFFGROUP {CutoffGroupStamp* currCutoffGroupStamp = new CutoffGroupStamp(); blockStack.push(currCutoffGroupStamp);}
244			(cutoffgroupstatement)*
245			ENDBLOCK ) {
246			blockStack.top()->validate();
247			blockStack.pop();
248			MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
249			currMoleculeStamp->addCutoffGroupStamp(currCutoffGroupStamp);
250			}
251			;
252
253			cutoffgroupstatement
254			{
255			vector<int> ivec;
256			CutoffGroupStamp* currCutoffGroupStamp = static_cast<CutoffGroupStamp*>(blockStack.top());
257			}
258			: assignment
259			\| #(MEMBERS ivec=inttuple) {currCutoffGroupStamp->setMembers(ivec);}
260			;
261
262			fragmentblock {int ival;}
263			: #(FRAGMENT ival=intConst {FragmentStamp* currFragmentStamp = new FragmentStamp(ival); blockStack.push(currFragmentStamp);}
264			(fragmentstatement)*
265			ENDBLOCK) {
266			blockStack.top()->validate();
267			blockStack.pop();
268			MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
269			currMoleculeStamp->addFragmentStamp(currFragmentStamp);
270			}
271			;
272
273			fragmentstatement : assignment
274	gezelter	1776	;
275	tim	770
276
277
278	gezelter	1776	doubleNumberTuple returns [vector<RealType> dvec]
279	tim	770	{
280	gezelter	1776	RealType dval;
281			}
282			: (dval=doubleNumber {dvec.push_back(dval);})+
283			;
284
285
286			inttuple returns [vector<int> ivec]
287	tim	770	{
288	gezelter	1776	int ival;
289	tim	770	}
290	gezelter	1776	: (ival=intConst {ivec.push_back(ival);})+
291			;
292	tim	770
293			protected
294			intConst returns [int ival]
295	gezelter	1776	: i1:NUM_INT {ival = lexi_cast<int>(i1->getText());}
296			\| i2:NUM_LONG {ival = lexi_cast<int>(i2->getText());}
297			;
298	tim	770
299			protected
300	gezelter	1776	doubleNumber returns [RealType dval]
301			: ic:intConst {dval = lexi_cast<RealType>(ic->getText());}
302			\| fc:floatConst {dval = lexi_cast<RealType>(fc->getText());}
303			;
304	tim	770
305			protected
306	tim	963	floatConst returns [RealType dval]
307	gezelter	1776	: d1:NUM_FLOAT {dval = lexi_cast<RealType>(d1->getText());}
308			\| d2:NUM_DOUBLE {dval = lexi_cast<RealType>(d2->getText());}
309			;
310